Enhanced Sampling of Phase Transitions in Coarse-Grained Lipid Bilayers

2017 ◽  
Vol 121 (23) ◽  
pp. 5770-5780 ◽  
Author(s):  
David Stelter ◽  
Tom Keyes
Keyword(s):  
Phase Transitions ◽  
Lipid Bilayers ◽  
Coarse Grained ◽  
Enhanced Sampling

PEG blocking of single pores arising on phase transitions in unmodified lipid bilayers

BIOPHYSICS ◽  
2008 ◽  
Vol 53 (5) ◽  
pp. 390-395 ◽  
Author(s):  
V. F. Antonov ◽  
E. Yu. Smirnova ◽  
A. A. Anosov ◽  
V. P. Norik ◽  
O. Yu. Nemchenko
Keyword(s):  
Phase Transitions ◽  
Lipid Bilayers

scholarly journals In Silico Study of the Mechanism of Binding of the N-Terminal Region of α Synuclein to Synaptic-Like Membranes

Life ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 98 ◽  
Author(s):  
Carlos Navarro-Paya ◽  
Maximo Sanz-Hernandez ◽  
Alfonso De Simone
Keyword(s):  
Lipid Bilayers ◽  
Conformational Transition ◽  
Md Simulations ◽  
Bound State ◽  
Terminal Region ◽  
Coarse Grained ◽  
Biological Behavior ◽  
In Silico Study ◽  
Membrane Bound ◽  
Presynaptic Protein

The membrane binding by α-synuclein (αS), a presynaptic protein whose aggregation is strongly linked with Parkinson’s disease, influences its biological behavior under functional and pathological conditions. This interaction requires a conformational transition from a disordered-unbound to a partially helical membrane-bound state of the protein. In the present study, we used enhanced coarse-grained MD simulations to characterize the sequence and conformational determinants of the binding to synaptic-like vesicles by the N-terminal region of αS. This region is the membrane anchor and is of crucial importance for the properties of the physiological monomeric state of αS as well as for its aberrant aggregates. These results identify the key factors that play a role in the binding of αS with synaptic lipid bilayers in both membrane-tethered and membrane-locked conformational states.

scholarly journals Metadynamics studies of crystal nucleation

IUCrJ ◽  
2015 ◽  
Vol 2 (2) ◽  
pp. 256-266 ◽  
Author(s):  
Federico Giberti ◽  
Matteo Salvalaglio ◽  
Michele Parrinello
Keyword(s):  
Molecular Dynamics ◽  
Phase Transitions ◽  
State Of The Art ◽  
Sampling Technique ◽  
Short Review ◽  
Crystal Nucleation ◽  
Crystalline Solid ◽  
Enhanced Sampling ◽  
Long Timescales ◽  
Direct Investigation

Crystallization processes are characterized by activated events and long timescales. These characteristics prevent standard molecular dynamics techniques from being efficiently used for the direct investigation of processes such as nucleation. This short review provides an overview on the use of metadynamics, a state-of-the-art enhanced sampling technique, for the simulation of phase transitions involving the production of a crystalline solid. In particular the principles of metadynamics are outlined, several order parameters are described that have been or could be used in conjunction with metadynamics to sample nucleation events and then an overview is given of recent metadynamics results in the field of crystal nucleation.

Interactions of peripheral proteins with model membranes as viewed by molecular dynamics simulations

2014 ◽  
Vol 42 (5) ◽  
pp. 1418-1424 ◽  
Author(s):  
Antreas C. Kalli ◽  
Mark S. P. Sansom
Keyword(s):  
Lipid Bilayers ◽  
Molecular Mechanisms ◽  
Phospholipid Composition ◽  
Md Simulations ◽  
Multiscale Simulation ◽  
Lipid Binding ◽  
Coarse Grained ◽  
Peripheral Proteins ◽  
Dynamics Simulations ◽  
Phosphatidylinositol Phosphates

Many cellular signalling and related events are triggered by the association of peripheral proteins with anionic lipids in the cell membrane (e.g. phosphatidylinositol phosphates or PIPs). This association frequently occurs via lipid-binding modules, e.g. pleckstrin homology (PH), C2 and four-point-one, ezrin, radixin, moesin (FERM) domains, present in peripheral and cytosolic proteins. Multiscale simulation approaches that combine coarse-grained and atomistic MD simulations may now be applied with confidence to investigate the molecular mechanisms of the association of peripheral proteins with model bilayers. Comparisons with experimental data indicate that such simulations can predict specific peripheral protein–lipid interactions. We discuss the application of multiscale MD simulation and related approaches to investigate the association of peripheral proteins which contain PH, C2 or FERM-binding modules with lipid bilayers of differing phospholipid composition, including bilayers containing multiple PIP molecules.

Aggregation and insertion of melittin and its analogue MelP5 into lipid bilayers at different concentrations: effects on pore size, bilayer thickness and dynamics

2017 ◽  
Vol 19 (10) ◽  
pp. 7195-7203 ◽  
Author(s):  
Sun Young Woo ◽  
Hwankyu Lee
Keyword(s):  
Pore Size ◽  
Lipid Bilayers ◽  
Force Fields ◽  
Coarse Grained ◽  
Bilayer Thickness ◽  
Molar Ratios

Melittin and its analogue MelP5 (five mutations T10A, R22A, K23A, R24Q, and Q26L of melittin) were simulated with lipid bilayers at different peptide/lipid molar ratios using all-atom and coarse-grained (CG) force fields.

scholarly journals Formation of adhesion domains in stressed and confined membranes

Soft Matter ◽  
2015 ◽  
Vol 11 (19) ◽  
pp. 3780-3785 ◽  
Author(s):  
Nadiv Dharan ◽  
Oded Farago
Keyword(s):  
Surface Tension ◽  
Lipid Bilayers ◽  
Computer Simulations ◽  
Molecular Model ◽  
Coarse Grained ◽  
Supported Lipid Bilayers

We use computer simulations of a coarse-grained molecular model of supported lipid bilayers to study the formation of adhesion domains in confined membranes, and in membranes subjected to a non-vanishing surface tension. When the membrane is subjected to compression, the condensation of the adhesion domains triggers membrane buckling.

Sign in / Sign up

Export Citation Format

Share Document